Bioinformatics – Functional Genomics – Dr. Víctor Treviño
El metaboloma Representa la colección de todos los metabolitos de un organismo biológico Productos de función y expresión genética
SeparationDetection SampleSignal Gas chromatography (GC) High performance liquid chromatography (HPLC) Capillary electrophoresis (CE) Ultra-high pressure liquid chromatography (UPLC) Ion mobility Matrix-assisted laser desorption/ionization (MALDI) … Mass Spectrometry (mass-to-charge ratio) Fourier transform ion cyclotron resonance (FTMS) … NMR based detection Sample Signal nuclei spin resonance
NMR experiments is very quick NMR equipment is quite expensive MS is more sensitive than NMR MS spectra can be wider than NMR
MS:m/z NMR:ppm [concentration] Visualization: 1 – Sample Example: TIC – Total Ion Counter
Los tiempos de retención de muchos metabolitos son conocidos Otros se pueden aislar apartir del “pico” y luego estudiar para identificar
The Handbook of Metabonomics and Metabolomics (2007) – JeremyK. Nicholson, Elaine Holmes and John C. Lindon
Processing methods for differential analysis of LC-MS profile data - katajamaa - Oresic - BMC Bioinf 2005 Σ
MS:m/z NMR:ppm [concentration] Visualization: 1 – Sample Example: TIC – Total Ion Counter
MS:m/z NMR:ppm [concentration] Several Samples
Bins Samples BINS
Base line correction Phasing / Alignment Solvent Peak NMR : TSP, … (3-trimethylsilylpropionic acid) MS : Water Standard pH shifts Temperature Effects
Base-Line Subtraction Suavizado Moving Average Used for smoothing No data reduction Overlapping windows Binning Used for smoothing… … and data reduction Non overlapping windows window size … … Integración
Phase Alignment Scale
1. Corrección de línea base (remoción de background) 2. Suavizado (smoothing) 3. Binning (disminución de datos y suavizado) 4. Alineamiento de Picos 5. Normalización de Escala
Hierarchical Clustering (similar to Transcriptomics but using only sample clustering) PCA – Principal Component Analysis - Que software ya conocido podemos usar? MeV
Untargeted large-scale plant metabolomics using liquid chromatography coupled to mass spectrometry - De Vos - Hall - Nat Prot 2007